Goal: count SNP difference between LTR and LTNR on a per gene basis
library(tidyverse)
library(ggrepel)get the vcf header
vcf.header <- system("zgrep '#C' ../input/LT.vcf.gz",intern = TRUE)
vcf.header[1] "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t38LTR\t42LTR\t42LTRR\t43LTR\t43LTRR\t49LTWR\t49LTWRR\t95LTWR\t95LTWRR\t99LTWR"vcf.header <- vcf.header %>%
str_replace("#","") %>% #get rid of the pound sign
str_split(pattern = "\t") %>% #split on the tabs
magrittr::extract2(1)
vcf.header [1] "CHROM" "POS" "ID" "REF" "ALT" "QUAL" "FILTER" "INFO"
[9] "FORMAT" "38LTR" "42LTR" "42LTRR" "43LTR" "43LTRR" "49LTWR" "49LTWRR"
[17] "95LTWR" "95LTWRR" "99LTWR" get the data
snps <- read_tsv("../input/LT.vcf.gz", na = c("","NA","."),comment="#",col_names = vcf.header) %>%
select(-ID, -FILTER) # these are empty columnsParsed with column specification:
cols(
CHROM = col_character(),
POS = col_integer(),
ID = col_character(),
REF = col_character(),
ALT = col_character(),
QUAL = col_double(),
FILTER = col_character(),
INFO = col_character(),
FORMAT = col_character(),
`38LTR` = col_character(),
`42LTR` = col_character(),
`42LTRR` = col_character(),
`43LTR` = col_character(),
`43LTRR` = col_character(),
`49LTWR` = col_character(),
`49LTWRR` = col_character(),
`95LTWR` = col_character(),
`95LTWRR` = col_character(),
`99LTWR` = col_character()
)
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|===========================================================================| 100% 398 MBsnpsremove 38LTR
snps <- snps %>% select(-`38LTR`)filter to keep snps where there is data from all samples
snps <- snps %>%
filter({select(., matches("[0-9]")) %>% complete.cases() })
snpssnps <- snps %>%
mutate(TOTAL_DEPTH= {str_extract(INFO, "DP=[0-9]*") %>%
str_remove("DP=") %>%
as.numeric() }
) %>%
filter(QUAL >=100,
nchar(ALT)==1,
TOTAL_DEPTH > quantile(TOTAL_DEPTH, 0.05),
TOTAL_DEPTH < quantile(TOTAL_DEPTH, 0.95))
snpsunpack the information differnet samples:
samples <- colnames(snps) %>% str_subset("^[0-9]")
for (s in samples) {
snps <- snps %>%
separate(!!s, into=paste(s,c("gt","tot.depth","allele.depth","ref.depth","ref.qual","alt.depth","alt.qual","gt.lik"),sep="_"),
sep=":", convert = TRUE)
}
snpsnext steps
keep snps that are fixed differences between LTRR and LTNR
Count per gene
first, convert to long format
snps.l <- snps %>% select(CHROM, POS, ends_with("_gt")) %>%
gather(key="plant", value="gt", -CHROM, -POS) %>%
mutate(response=str_extract(plant, "(LTR|LTWR)")) %>%
arrange(CHROM, POS, response, plant)
snps.lfilter to keep homozygous and fixed
n.samples <- length(unique(snps.l$plant))
unique(snps.l$gt)[1] "0/1" "1/1" "0/0"snps.l <- snps.l %>%
filter(gt != "0/1") %>% # keep homozygous
group_by(CHROM, POS, response) %>%
filter(length(unique(gt))==1) %>% # all samples for a given response have the same genotype
group_by(CHROM,POS) %>%
filter(n() == n.samples) %>% # have a gt from every plant
filter(length(unique(gt))==2) %>% # different genotypes in LTR and LTWR
arrange(CHROM, POS, response, plant)
snps.lsummarize per gene
snp.summary <- snps.l %>%
group_by(CHROM) %>%
summarize(snps=n() / n.samples) %>%
rename(contig=CHROM)
snp.summary %>% arrange(desc(snps))snp.summary %>% arrange(desc(snps)) %>%
write_csv("../output/fixed_snps.csv")